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LOC122847308 Sharpr-MPRA regulatory region 13497 [ Homo sapiens (human) ]

Gene ID: 122847308, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122847308
Gene description
Sharpr-MPRA regulatory region 13497
Gene type
biological region
Feature type(s)
regulatory: silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Oct 2021]
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Genomic context

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See LOC122847308 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (164061159..164061453)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (164518432..164518726)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (164917669..164917963)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985829 Neighboring gene uncharacterized LOC105373728 Neighboring gene VISTA enhancer hs170 Neighboring gene NANOG hESC enhancer GRCh37_chr2:164478034-164478535 Neighboring gene Sharpr-MPRA regulatory region 10417 Neighboring gene uncharacterized LOC107985957 Neighboring gene fidgetin, microtubule severing factor Neighboring gene VISTA enhancer hs640 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:164593125-164593641 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:164593642-164594157 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:164627636-164628835 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:164765722-164766240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:164766241-164766758 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:164809702-164810901 Neighboring gene VISTA enhancer hs421 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16724 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:165027147-165027366 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16725 Neighboring gene phosphoribosyl pyrophosphate synthetase 1 pseudogene 1 Neighboring gene cytochrome P450 family 2 subfamily C member 56, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, Free PMC Article

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_077043.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    164061159..164061453
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    164518432..164518726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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